The SMRTbell gDNA Sample Amplification Kit enables whole genome amplification starting from as little as 5 ng of genomic DNA. It’s one of the questions we hear most often from scientists working with small organisms: Is it possible to generate truly high-quality, long-read data from minuscule amounts of DNA? With our new kit for ultra-low DNA input projects, the answer is: Absolutely! The new workflow dramatically reduces the requirements for DNA quantity. Now, scientists need only 5 ng of genomic DNA to kick off a SMRT Sequencing project — that’s less than 2% of the starting volume needed for our…
With PacBio HiFi sequencing data now readily available for organisms of any size, many exciting results have been published featuring new de novo assembly methods optimized for highly accurate long reads. These methods have produced assemblies for a variety of organisms at quality levels never before thought possible — as measured by completeness, contiguity and correctness. We feel privileged to collaborate with the scientific community on the development of these tools. From Small to Tall When the USDA wanted to rapidly assemble the Asian Giant Hornet as part of its real-time invasive species response initiative, they turned to a tool…
A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. It has recently become apparent how important it is to sequence more than one individual to characterize the genomic variation within a species. This makes sense if you consider that sexually reproducing organisms are a mix of their parents and, therefore, not identical. This is just as true in crops as it is in humans. So, it’s not surprising that when a group of researchers from several institutions in China embarked on de novo genome assemblies of several accessions of…
How do bacteria manipulate plant biology to cause blight and rot? Why are some pathogen strains more virulent than others? How can we engineer resistant staple food crops? These are pressing questions facing researchers looking to sustain and increase crop production against the backdrop of a changing environment. For one major clade of pathogens, Xanthomonas spp, the answers lay locked within TAL effector genes (TALEs), but assembling these highly variable, repetitive regions was a long-standing obstacle. The key to finally unraveling the tangled assemblies was PacBio long-read sequencing. Code-breaker Adam J. Bogdanove from Cornell University. Photo by Jesse Winter Plant…
With a nickname like “murder hornet,” it’s no wonder the two-inch long Asian giant hornet (Vespa mandarinia) has caused a stir amongst those terrified of insect invasions. Various species of paper wasp (left) compared to the Asian giant hornet (right) Photo by Hanna Royals, USDA. The wasps — which are actually more dangerous to bees than humans — have made another recent appearance in Washington state, and Agricultural Research Service (ARS) scientists are hoping a new rapidly-generated genome sequence of one of the insects will help in their quest to quash an invasion. Released August 6, the first high-quality genome…
Tackling larger and larger genomes has been an attractive pursuit for many scientists as sequencing technologies improve at rapid rates. But what about the other end of the spectrum — the tiny organisms that comprise much of the diversity of life? An obvious obstacle to decoding the DNA of small organisms such as insects, nematodes and other arthropods is collecting enough of it to actually sequence (usually multiple micrograms worth). Until recently, the solution was to pool DNA from many of these tiny creatures to create a representative sample, and extrapolate the biology of the individual constituents from there. But…
The new and updated species in Ensembl 99 from the Vertebrate Genomes Project (VGP) Meerkats, yaks, geese, and lots of flies — oh my! A full menagerie of new and updated animal genomes has been released by the Ensembl project. The Ensembl 99 release includes a variety of vertebrates, plants, mosquitos, and flies, as well as updates of human gene annotation and variation data. Among them are 38 new species and two dog breeds (Great Dane and Basenji), as well as four updated genome assemblies. Many were created using PacBio sequencing data. Thirteen of the new assemblies have…
Matt Hufford, associate professor at Iowa State University, helped produce a 26-line maize pangenome assembly collection Maize researchers have been rejoicing over a New Year’s gift delivered by a group of 33 scientists: A 26-line “pangenome” reference collection. The multi-institutional consortium of researchers used the Sequel System and BioNano Genomics optical mapping to create the assemblies and high-confidence annotations. They released the results on January 9, and in several presentations at the Plant and Animal Genome XXVIII Conference, less than two years after the ambitious project was funded by a $2.8 million National Science Foundation grant. The collection includes comprehensive,…
With the release of the award-winning Sequel II System, 2019 was an exciting year for the SMRT Sequencing community. We were inspired by our users’ significant contributions to science across a wide range of disciplines. As the year draws to a close, we have taken this opportunity to reflect on the many achievements made by members of our community, from newly sequenced plant and animal species to human disease breakthroughs. “It has been another phenomenal year for science. The introduction of the Sequel II System will accelerate discovery even more, and I can’t wait to see what 2020 will…
Photo of a pale spear-nosed bat (Phyllostomus discolor) courtesy of the Rossiter Lab (@rossiterlab) Bat lovers and animal researchers have been waiting for insights into the evolution and remarkable genetic adaptations of our winged mammalian friends, ever since the global Bat1K initiative announced its quest to decode the genomes of all 1,300 species of bats using SMRT Sequencing and other technologies. Now, the first six reference-quality genomes have been released on the Hiller Lab Genome Browser, and described in a pre-print by Sonja Vernes (@Sonja_Vernes), Michael Hiller (@hillermich) and Gene Myers (@TheGeneMyers) of the Max Planck Institute, Emma Teeling (@EmmaTeeling1) of…
There’s the genome, the transcriptome, the microbiome… and now the NLRome? Breeders and pathologists have long been interested in uncovering the secrets of plant immunity, and much of their attention has been focused on receptors that can activate immune signalling: cell-surface proteins that recognize microbe-associated molecular patterns (MAMPs), and intracellular proteins that detect pathogen effectors, including nucleotide-binding leucine-rich repeat receptors (NLRs). Hundreds of NLR genes can be found in the genomes of flowering plants. They are believed to form inflammasome-like structures, or resistosomes, that control cell death following pathogen recognition, and are being investigated as candidates for engineering new pathogen…
A team of Japanese researchers has used a new Pacific bluefin tuna reference genome to identify male-specific DNA markers in the fish The cultivation and conservation of one of the most important commercial fishes in the world may come down to sex determination — how can you successfully breed a species without knowing the sex of your stock? A Japanese research team has come up with a solution, thanks to a new Pacific bluefin tuna reference genome and the male-specific DNA markers they were able to identify as a result. In a study published recently in the Nature journal Scientific…
It was the coolest critter Erin Bernberg (@ErinBernberg) had ever worked with – quite literally. The senior scientist at the University of Delaware Sequencing and Genotyping Center, a PacBio certified service provider, received a shipment of tiny, live ice worms from Washington State University and immediately faced several challenges. How would she get them out of their ice cubes? How would she isolate DNA from the delicate, dark pigmented creatures? And would she be able to extract enough DNA to sequence? Thanks to the new PacBio low DNA input protocol, the answer to the last question was yes. In fact,…
Seeking to sequence and characterize entire transcriptomes in one go? Our new Iso-Seq protocol and reverse-transcriptase PCR kit makes it easier, speedier and cheaper. Run on the new Sequel II System, the completely revamped Iso-Seq Express workflow achieves whole transcriptome characterization from a single SMRT Cell 8M delivering up to 400 Gb, and at a third of the cost, or less. Yield has also increased on the Sequel System, with 3.0 sequencing chemistry typically delivering up to 30 Gb per SMRT Cell 1M for our RNA sequencing application. The new protocol requires three times less RNA input (300 ng) and…
Single Molecule, Real-Time (SMRT) Sequencing continues to get smarter and more powerful, with the recent launch of the Sequel II system increasing capabilities and efficiencies of the long-read DNA and RNA PacBio sequencing technology even further. In a special issue devoted entirely to the technology in the MDPI open access journal Genes, guest editors Adam Ameur of Uppsala University and Matthew S. Hestand of the Cincinnati Children’s Hospital Medical Center present eight articles highlighting research conducted using SMRT Sequencing. As this special issue demonstrates, the benefits of SMRT Sequencing to many different areas of research are becoming evident, not only…